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comparison trimmomatic.xml @ 14:d94aff5ee623 draft

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Version 0.38.1: add coreutils as dependency to fix tool issues with 'readlink -e' across platforms.
author pjbriggs
date Thu, 26 Mar 2020 04:52:47 -0400
parents 898b67846b47
children 32f1f56bd970
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13:898b67846b47 14:d94aff5ee623
1 <tool id="trimmomatic" name="Trimmomatic" version="0.38.0"> 1 <tool id="trimmomatic" name="Trimmomatic" version="0.38.1">
2 <description>flexible read trimming tool for Illumina NGS data</description> 2 <description>flexible read trimming tool for Illumina NGS data</description>
3 <macros> 3 <macros>
4 <import>trimmomatic_macros.xml</import> 4 <import>trimmomatic_macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="0.38">trimmomatic</requirement> 7 <requirement type="package" version="0.38">trimmomatic</requirement>
8 <!--
9 Coreutils required for 'readlink -e' work across platforms
10 See similar fix for snpSift
11 https://github.com/galaxyproject/tools-iuc/commit/b5e2080a7afdea9fa476895693b6115824c6fbb9
12 -->
13 <requirement type="package" version="8.25">coreutils</requirement>
8 </requirements> 14 </requirements>
9 <command detect_errors="aggressive"><![CDATA[ 15 <command detect_errors="aggressive"><![CDATA[
10 @CONDA_TRIMMOMATIC_JAR_PATH@ && 16 @CONDA_TRIMMOMATIC_JAR_PATH@ &&
11 @CONDA_TRIMMOMATIC_ADAPTERS_PATH@ && 17 @CONDA_TRIMMOMATIC_ADAPTERS_PATH@ &&
12 #if $readtype.single_or_paired == "pair_of_files" 18 #if $readtype.single_or_paired == "pair_of_files"